Altered
by Some Douche
Summary: What if the seal was designed to alter Naruto's chakra? However, this has it's consequences, both good, and bad. Slight AU.
1. Chapter 1

Well, hello there, you should know this is my first fanfic, so constructive criticism would be greatly appreciated.

Disclaimer: Naruto is the property of Masashi Kishimoto, I'm just some guy who liked the series (Pre-War Arc, that is).

So, without further ado, I present:

 **Altered**

It had been five years. Five years since hundreds, nay, thousands of voices, mothers, fathers, sons, daughters, shinobi, civilian, were silenced. In a single night, Konohagakure lost so much.

Among the losses, was Minato Namikaze, Fourth Hokage, a young man, who had spiky blond hair, blue eyes, and a white cloak, adorned in flames, a prodigy only seen once a generation, loved by the people, and a war hero.

All of this caused by the Kyuubi no Yoko, a beast that, with a strike of it's tail, could cause tidal waves, and with one roar, sow fear into the heart of even the most stoic man.

It was only stopped by The Fourth, who, sacrifing his soul to the Shinigami, sealed the beast inside of a small blond child named Naruto Uzumaki.

And this, ladies and gentlemen, is where our story truly begins.

 **Konoha**

Morning was breaking in Konoha, birds were chirping, people were waking up, and the first signs of shinobi activity were starting to show. One person in particular, however, was Naruto Uzumaki, five years old, energetic, cheerful, and (unknowing) demon container, was waking up.

Little Naruto got out of bed, along with the other children at the orphanage, they slept in a medium sized room, full of bunk beds, all of them rather close together, and begun their morning routine.

After that, the children were taken to a playground area by the caretakers, where there were some swings, a slide, a sandbox, the usual.

Naruto was usually excluded by the other children, although not apparently on purpose. They simply didn't let him play with them, or just seemed to treat him like he wasn't there. It was annoying, but when Naruto tried to talk to the caretakers, they told him they were too busy.

Naruto for the most part didn't mind it too much, sure, he wanted to play with them, but after a year or two of getting excluded, it was hard to care. Besides, who needed them when once every month the Hokage himself came to visit Naruto, heck he even took him out for ramen, and last time he'd even taught him a cool trick!

He remembered the day the Hokage had taught it to him.

 **Flashback**

 _It was evening, and two figures sat, one an old man, wearing a white robe covered in red markings, with a red hat with the kanji for fire on the front, his wizened, wrinkled, calmly smiling face spoke of wisdom earned over a lifetime full of hard earned success. The other, a small child, wearing a white shirt with a red spiral, and light brown shorts, happily eating a bowl of ramen, soon to be added to the quickly building pile of empty ones at his right._

 _This one's face (which possessed some odd whisker markings) was full of innocence, naivete, joy, and was also covered in ramen broth._

" _So, Naruto, I heard you wanted to become a ninja?" Questioned the Hokage._

" _Of course! I mean, ninjas are so_ _ **cool**_ _, dattebayo! Making fireballs, blowing things up, rescuing princesses, and you're the strongest one, right? And how do you guys do all that, Jiji? The child excitedly, and rapidly, asked._

 _Chuckling lightly, the Hokage responded: "Now, now, Naruto, one thing at a time. First off, refer to me as Hokage-sama, or at the very least Hokage, second of all, yes, I am the strongest ninja currently alive. But, Naruto, you must understand that being a ninja isn't all fun and games, there is great danger, and all power begets responsibility. And, last of all, ninjas use chakra."_

" _Chakra?"_

" _Yes, chakra is something present in all living things, and is easily described as the life force of all things, everyone has chakra, and it is necessary to survival, however, ninjas train themselves to have excess chakra, and use it in jutsu, such as fireball." The Hokage explained in a sagely manner._

" _Oohh. Could you teach me?!"_

" _Well Naruto, how about a little trick. Close your eyes, and imagine you had water in your belly, and then try to move that water into your arm."_

 **End Flashback**

And so he had, at first it was difficult, as he just couldn't push the water, but slowly over weeks of constant failed attempts, he succeded, and it felt … odd.

It was like if his arm was full of water, and it started leaking, it felt painful, and when he opened his eyes, strange, ethereal blue threads were escaping his arm, he, unsuccessfully, tried to grab them, but they just went through his fingers.

He tried the same thing, only now on his other arm, but now with wide open eyes, just brimming with wonder, curiosity and excitement, and sure enough, the feeling of being full of water, of it starting to leak, and the blue threads poured out again.

With a wide grin, Naruto jumped, his fist held up in the air, shouting: "Yatta!".

A.N.: Well, hope that wasn't awful for you, please review, and let me know what you think. Also, for those wondering, there's a reason Naruto's chakra is visible, it's just that this fic is going to be a bit slow. Thank you, and have a nice day.


	2. Chapter 2

A.N. Thank you so much for the reviews, as for the reason why Naruto's chakra is visible, well, it'll be explained later.

Disclaimer: I don't own Naruto, Kishimoto does.

 **Altered**

Naruto was, once again, sitting alone on the playground, ignored by everyone, still doing the exercise Sarutobi had taught him.

And, once again he looked at the odd, softly glowing blue wisps coming from his arm. Naruto was amazed, but confused. Was this chakra? The "thing ninjas use for everything" chakra?

It seemed so…but…why couldn't he touch it? Whenever he tried to, his fingers just passed through it like smoke. How could ninjas breathe fire, make tornados, and all kinds of things with this?

He'd have to ask the old man about it later, for now, he just kept pulling the "water" to his right arm.

Naruto took a week to do it the first time, but now he had the rest the month to go. So, he started trying to do the trick on his other arm. He succeeded after two days, and, lo and behold same thing happened, light blue smoke.

Then, after another few days, he got it to work on his legs… nothing new. Then, on his face, and, again, nothing new.

So… Naruto, only a day before the Hokage's next visit, tried to do it on his whole body.

Naruto was having trouble, pulling chakra from his belly, and dividing it for the whole body, as it turned out, was hard. But still, he persevered, slowly the smoke started coming from each limb, appearing in ghostly, otherworldly, and softly glowing blue.

Naruto then felt something burn in his stomach, like the "water" had now been replaced by scalding steam.

Naruto tried to stop pulling his chakra, but it was in vain, this _thing_ just seemed to be forcing itself through his veins, and it hurt, like if he was burning from the inside out.

The worst came when it reached his head. When it reached the throat, it was like something was choking him, when it reached his mouth, it felt like drinking boiling water, and when it reached his eyes, it was like having acid dumped over them.

The once blue, soft, calmly rising threads were replaced with red, swirling, and goo like waves.

The red chakra seemed to quickly take shape and fade away just as fast, taking the form of faces with sharp teeth, and long tongues going across exposed skin, large, clawed hands, squeezing at places, and, with uncanny strength, breaking bone.

Naruto could vaguely hear screams, both from adults and children, and then, the violent red shroud wrapped around him, thick as stone, yet as fluid as water, and he saw red, before blacking out.

 **Linebreak-**

Naruto woke up abruptly, he was breathing deeply, sweating bullets, and his head seemed like it was going to explode at any minute now.

Observing his surroundings, Naruto found himself in a plain, completely bare white room, in a rough, hard bed.

" _Where am I? And what was that? W-was it just a dream?"_ The child thought to himself.

Before he could dwell on those thoughts, the door opened, revealing the Hokage, along with two animal masked ninja.

"Hello Naruto-kun." The Hokage said, with an imperceptible twang of worry in his voice.

"O-old man! You're here! Where am I? And what happened?" The young boy said, failing to hide his worry and fear.

The Hokage made a long, pained sigh. Nevertheless, he braced himself for what he was about to do.

"Naruto, have you ever heard about the Kyuubi?"

"Y-yeah, it attacked the village five years ago, and was killed by the Fourth, y'know?" Naruto answered, unsure how this was related to what was going on.

"Not quite." Naruto tilted his head in confusion. "The Kyuubi is one of nine demons, known as Tailed Beasts, these creatures are made purely of chakra, and, in turn, cannot be permanently dealt with."

Sarutobi looked to Naruto, to see if he was following what was being said.

"However, they can be sealed."

"Sealed?" Naruto asked in confusion.

"Yes…" Pulling out a scroll from one of his pockets, the Hokage opened it, and showed him an odd writing on it. "…this, is a seal, sealing is one of the less practiced ninja arts, to summarize, it manipulates chakra with written seals instead of handsigns."

Pulling out a kunai, Sarutobi continued. "Imagine this kunai is Kyuubi…" the Hokage channeled chakra into the seal, and, with a poof, the kunai was gone.

"Wait, what? Where did it go?"

Sarutobi guided his chakra to the seal, and with another poof, the kunai was back in his hand. "In the seal."

"That's awesome! But…what does this have to do with me again?"

"Well, since the Tailed Beasts are sentient, you can't seal them in an object, as, eventually, they'll break out, so, they have to be sealed in a person, and these people are called Jinchuuriki."

"Huh-uh." Naruto was listening closely, and was rather slowly connecting the dots.

"Naruto-kun, you are a jinchuuriki."

A.N.: Oh boy, this was a chapter. The red chakra was indeed Kyuubi's, why it came in so suddenly will be explained next time. Also, if you think the description was too violent, that was to set up how Kyuubi chakra works with this "altered" Naruto. As always, please review, and have a nice day.


	3. Chapter 3

A.N.: Hello dear readers, it's me again. First of all, I've been listening to my reviewers, and I shall be making longer chapters from now on, second of all, for some of you wondering, Kyuubi hasn't given Naruto a bloodline exactly, I'll leave the specifics to the chapter. Without much further ado:

 **Altered**

In a bare white room, on a simple bed, sat Uzumaki Naruto, Jinchuuriki of the Kyuubi, as he'd just learnt, with wide eyes and mouth agape.

"I'm a…Jinchuuriki?" Said Naruto, more in sheer disbelief than anything else.

"Calm down Naruto-kun…" Sarutobi said, while pulling the child into a hug. "…Naruto, I want to help you, O.K.?" The Hokage looked at the boy with a reassuring smile. "No matter what anybody says, you aren't the Fox, you're Uzumaki Naruto, understood?".

"O.K. then old ma- I mean, Hokage-sama, dattebayo." Naruto said. The boy was thinking over those words. Yeah, the old man was right, he wasn't a demon fox! He was Naruto!

"With that out of the way, Naruto, could you tell me what you remember before going unconscious?"

"Huh, well, I was channeling chakra like you told me to, but on my whole body instead of just the arms, when this weird red stuff appeared, and it felt awful, like it was alive and tryin' to kill me or something! I saw this weird flash of red…and that's it." The boy said, wincing at the memory.

"Naruto-kun, that "red stuff" was Kyuubi's chakra." Hiruzen told the boy.

"Wait, seriously?" Naruto said. "It can do that?"

"Yes, a jinchuuriki is inherently connected to the beast through their seal, this potentially make the container able to wield the demon's power, but at risk of possession." Sarutobi carefully explained. "However, the seal you have, Naruto, is rather particular."

Naruto nodded, urging Sarutobi to go on.

"Your seal was designed by the Fourth himself, which, after going through some of his notes while making it, we found it was supposed to connect container and beast even closer, slowly mixing the monster's chakra with it's jinchuuriki's, and giving them much greater reserves, along with other benefits."

"Wait, I don't think I used the thing's power, so, how did it get me?" Naruto said, raising an eyebrow.

"While the Fourth was genius, he wasn't infallible, and the seal turned out to have unfortunate side effects. One of these, as you've experienced first hand, was giving the beast easy access to your chakra, letting it overwhelm you, and possess you."

"Then why did he use it?"

"As I said, the Fourth had designed it himself, and while he had studied other seals of this type, combined with the help of a Jinchuuriki, he had not yet used it practically."

"I still don't get it, if there were other seals, then why didn't he use those? Also, another Jinchuuriki?"

"Well, first off, the other Jinchuuriki was Kushina Uzumaki, ex container of the Kyuubi, part of the last remnants of her clan." Sarutobi said. "She was born with a rare mutation, which allowed her to mold her chakra into chains of gold, capable of subduing and containing chakra, since Tailed Beasts are wholly chakra, she was able to forcefully call on Kyuubi's power.

Sarutobi paused, as if hesitant. "This made her a formidable kunoichi, however, it angered the Fox, whose rage only grew. While it didn't harm Kushina, the next Jinchuuriki would be practically unable to use Kyuubi's power, at least, not without devolving into a mindless beast."

Naruto stood there, quietly listening, not letting his focus slip for even a second.

"So, as one of the most accomplished seal masters of all time, Minato Namikaze, future Fourth Hokage, had to fix this, his idea was to mix both chakras together, turning the container's chakra into mixture of human and demonic, which, while powerful in it's own right, would also let the Jinchuuriki grow accustomed with the beast's influence without putting them at risk."

"But it was never tested, because they couldn't." Said Naruto, eyes widening as he slowly spoke those words.

"On the night of the Kyuubi Attack, Kushina Uzumaki was murdered, and the assassin managed to release Nine Tails, letting it wreak havoc, before it was stopped by the Fourth, who hastily sealed it in a baby."

"Old- I mean, Hokage-sama, am I and this Kushina lady…related?" Naruto said, his eyes gleaming, and his voice hopeful.

It wasn't noticeable, but the Third gulped, took a deep breath, and prepared to lie through his teeth to a small child.

"No Naruto, her surname was given to you as an homage of sorts, as she did not leave any descendants, and you have "inherited" the fox from her."

"Oh…" He was quiet, the disappointment on his face was clear, but Naruto pulled himself together.

"So, why am I here?" Naruto asked.

"Well, the Fox attempted to take control, but a defense mechanism within the seal was activated, dispelling it's hold on you, but rendering you unconscious for two weeks."

"Two weeks?!" Naruto said, startled.

"Yes, turns out demonic possession is exhausting, anyway, after the incident, we needed to make sure you were okay, and if it really was "you" in there, or the Fox."

"Well, what happened to the orphanage?"

"Naruto-kun, most civilians, and even some shinobi, were already afraid, and after this incident, most them will think that you are unstable, or that you're just the Fox."

"But I'm fine, and besides, the worst I've ever did were some pranks, dattebayo!" Naruto protested, his naïve mind not fully understanding why they would suspect that of him.

"Yes, Naruto, I know, however, their judgement is clouded by fear, they do not look at you and see a child, but a living reminder of that day. Not only that, but if a simple academy exercise lets Kyuubi out, then you can't go to the academy."

"But if I don't go to the academy, then how do I become a ninja?" If he couldn't be a ninja, then he couldn't be Hokage, and if he couldn't be Hokage, he would never get acknowledged.

"Who said no one would? Let me remind you Naruto-kun, I am the Hokage of the most populous Hidden Village in all the Elemental Countries, if I don't can't do something, it's very doubtful anybody else can."

"Wait, old man, you're gonna teach me? Yatta!"

"Not me personally, but some of my shinobi can do it." He said, trying to calm down the blonde ball of energy beside him.

"Oh, O.K. then, but still, thanks a ton, old man, dattebayo!" He said jumping at the Hokage in a hug.

"Yes, one last thing." Naruto quirked his eyebrow at that, wondering what it could be. "Due to the villagers' distrust, you'll have to stay here, in this secluded compound." Sarutobi said, handing Naruto a map of the compound itself.

"This room is now yours, it will be furnished tomorrow, all your expenses, such as food, clothes, and water will be paid for." The Hokage said, before ruffling the child's hair. "Now I must go, I have things that need to be taken care of." As Hiruzen left, he wondered how the boy would do.

Naruto got up, suddenly taking notice of three bento boxes lying on a small table to his side. After eating one of them, he decided to explore the compound. Pulling the map from his pocket, he saw that he was near a training ground (Cool!), and a classroom (Boring!), there were some other rooms he glossed over, an armory, a garden, among others. One of the things these rooms shared with each other was that they all seemed connected by weird confusing corridors, seriously, the map outside the rooms looked like somebody just started drawing lines at random, while blindfolded, while gongs were being played inches from their ears.

Now, Naruto was reckless, thick skulled, and many other, less than flattering things, but he wasn't insane enough to go exploring someplace he barely knew, much less one that seemed to have more than three dimensions. Thankfully, there was a bathroom right beside his bedroom, so not all was lost.

Still, Naruto spent the whole day trying to make heads or tails of the map, to simply no avail, all it did was give him a headache. So, tired from seeing a map that didn't seem to be wholly from Kami-sama, Naruto bored himself to sleep by counting the ceiling tiles.

 **Linebreak** **-**

Waking up, Naruto found himself in what seemed like a different room, for it wasn't as bare as before, but now had a drawer, full of boring white shirts (which were just _begging_ to be painted orange), and bland dark green shorts (that _also_ needed to be orange), and blue striped pajamas in a corner was a fridge, with some food in it.

After getting dressed and eating his breakfast, Naruto heard someone knocking on his door. Opening it, Naruto faced a man wearing a bandana, round sunglasses, and standard jonin attire, except for the flak jacket.

"Hello, I am Ebisu, I will be your instructor for the foreseeable future, you may refer to me as sensei, any questions?" Said the newly introduced man, in a commanding and professional tone.

"Hi, I'm Uzumaki Naruto, dattebayo! Uh, where do we have "class"?" Naruto said, wondering if ninja even had regular classes.

"It shall be in the classroom, annotated on the map given to you, however, for the first semester, I will escort you there, as you're still accommodating yourself to this compound." Ebisu said, as he began walking along, urging Naruto to follow him.

The grey corridors of the compound, as far as Naruto could tell, all looked the same, he was wondering if they actually _were_ the same. Naruto had lost count of where they were by the twentieth turn to the right, as he was starting to think even his sensei didn't know where the classroom was!

Eventually, they saw a corridor, except at the very end of it was a white door.

When Ebisu opened it, Naruto found himself in a room painted light yellow, with a small table, various piles of supplies off to the corners of it, most of them looking rather sharp and pointy, and a bigger table next to a chalkboard, with wooden door off to the side.

"Take a seat." Ebisu said, pointing to the smaller table.

"Okay, but Ebisu-sensei! What are you gonna teach me? Is it walking on water? Shooting fireballs? What is it?" Naruto quickly said, sitting himself down, while failing to contain his excitement.

"None of that."

"Well then, what is it?"

Ebisu lamented his fate, stuck teaching this little brat, who didn't even have decent manners, mind you, how to be a ninja was going to be quite painful, but still, he had to soldier on, for the good of the village.

"Naruto, give me your arm."

"Uh, okay then, but what are you gonna do with it?"

Just as Naruto finished his question, it was answered, in a moment's notice, Ebisu was drawing a seal throughout his arm, telling him not to move, and as soon as he got done with, he asked for the other one.

"Sensei, why did you draw seals in my arm?"

"It is best if I show you."

Ebisu put a sewing needle and a leaf on the table, storing his brush.

"Now Naruto, you know how your chakra is "water", well, these seals are like filters, distilling certain parts of your chakra that we want to bring out."

"Got it, but what does that have to do with the leaf and the needle?"

"Well, Naruto I want you to channel chakra from your left arm into the leaf, then I will explain."

Following Ebisu's command, Naruto once again brought chakra to his arm, this time felling as if his chakra was being "distilled" by the seal, lightly touched the green leaf, and drove his chakra into it.

Before his very eyes, the leaf turned a dead brown color, starting from where he touched, and spreading to the rest, like a sickness, and, in but a moment the dead leaf, now starting to turn grey, became dust.

"What just happened!?" Naruto said bewildered by what he'd seen.

Then Ebisu picked up the needle, and pricked Naruto's right hand, drawing a tiny drop of blood.

"Ow! Why did you do that?" Naruto angrily said.

"Channel chakra to your hand." Ebisu said, ignoring the child's complaints.

"Fine." Naruto said, upset and doubtful of the man teaching him.

And again Naruto's chakra met his wound, only for it to close up, leaving only wisps of steam.

"Holy crap! That's awesome!" Naruto said, or rather, shouted at the top of his lungs.

Ebisu breathed deeply, and wondered how in the hell did the Hokage expect him to train this child. Nonetheless, he went on.

"I suppose you want to know how you're capable of this?" Naruto furiously nodded. "Well, as you may remember, Hokage-sama explained that the seal you have mixes your and demon's chakra, this as altered your chakra."

"Altered?" Naruto asked, raising his eyebrow.

"Yes, due to this mixing, your chakra has several properties typical of Bijuu chakra, such as being regenerative to themselves, and venomous to anything else, greater "density", and so on."

"So I get superpowers? Cool!"

"Not so fast, young man, although this might seem to be a net positive it is actually very restrictive. Due to your chakra's acidic nature, you may never use medical techniques, due to it's "density" it'll be useless for genjutsu, and because of it's mixed and unprecedented nature, many ninjutsu are going to be very complicated to perform or adapt to it."

Naruto was scratching his head in confusion, as he hadn't the slightest clue what any of that was. "So, is it bad?"

"Bad? Far from it, just different, and you must know, these restrictions have allowed Hokage-sama to create a more focused teaching plan for you."

"Focused, like what?"

"Well, being a Jinchuuriki, you have no shortage of chakra, in fact, as much as an elite jonin, so we can just drop that entirely, however, calling your control atrocious would be an understatement, so that's going to need a lot of work, while your other limitations and advantages give us some guidelines."

"I'll do my best, dattebayo!"

And so began Naruto's training.

A.N.: Hey there, I think I made the chapter too long, or too slow, but I really couldn't think of a better way to explain things than an exposition dump. Also, for those wondering, base Naruto will never even come close to being as powerful as Kyuubi, as that would be **very** overpowered. Next chapter will probably be a training montage. Anyway, thank you for reading, please review, and have a nice day.


End file.
